As the need for duplex stainless steel (DSS) increases, it is necessary to evaluate hydrogen stress cracking (HSC) in dissimilar welded joints (WJs) of DSS and carbon steel. This study aims to investigate the effect of the weld microstructure on the HSC behaviour of dissimilar gas-tungsten arc welds of DSS and carbon steel. In situ slow-strain rate testing (SSRT) with hydrogen charging was conducted for transverse WJs, which fractured in the softened heat-affected zone of the carbon steel under hydrogen-free conditions. However, HSC occurred at the martensite band and the interface of the austenite and martensite bands in the type-II boundary. The band acted as an HSC initiation site because of the presence of a large amount of trapped hydrogen and a high strain concentration during the SSRT with hydrogen charging. Even though some weld microstructures such as the austenite and martensite bands in type-II boundaries were harmless under normal hydrogen-free conditions, they had a negative effect in a hydrogen atmosphere, resulting in the premature rupture of the weld. Eventually, a premature fracture occurred during the in situ SSRT in the type-II boundary because of the hydrogen-enhanced strain-induced void (HESIV) and hydrogen-enhanced localised plasticity (HELP) mechanisms.